Hi,
When I try to use cluster program to cluster protein strucutres generated by rosetta ab-initio I get the following error:
ERROR: !pdb.empty()
ERROR:: Exit from: src/core/io/pdb/pdb_dynamic_reader.cc line: 208
I used following options:
cluster.linuxgccrelease -database /opt/rosetta/rosetta_database/
-in:file:l pdb-list
It looks like the PDB reader thinks your PDBs are empty. Not to be trivial, but are they? What's in your list pdb-list? (are they in the right directory?)